已下载不用重新去下载

wget http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-0.38.zip

解压安装

(base) 202031107010173@xiaoming-HP:~$ unzip /disk1/shares/Trimmomatic-0.38.zip -d ~/Biosofts/

运行测试及结果

(base) 202031107010173@xiaoming-HP:~$ java -jar ~/Biosofts/Trimmomatic-0.38/trimmomatic-0.38.jar
Usage:
       PE [-version] [-threads <threads>] [-phred33|-phred64] [-trimlog <trimLogFile>] [-summary <statsSummaryFile>] [-quiet] [-validatePairs] [-basein <inputBase> | <inputFile1> <inputFile2>] [-baseout <outputBase> | <outputFile1P> <outputFile1U> <outputFile2P> <outputFile2U>] <trimmer1>...
   or:
       SE [-version] [-threads <threads>] [-phred33|-phred64] [-trimlog <trimLogFile>] [-summary <statsSummaryFile>] [-quiet] <inputFile> <outputFile> <trimmer1>...
   or:
       -version

过滤原始数据

(base) 202031107010173@xiaoming-HP:~/Biosofts$ mkdir trim_out
(base) 202031107010173@xiaoming-HP:~/Biosofts$ java -jar ~/Biosofts/Trimmomatic-0.38/trimmomatic-0.38.jar PE -phred33 /disk/shares/Seqs/test_7942raw_1.fq.gz /disk/shares/Seqs/test_7942raw_2.fq.gz ./trim_out/output_forward_paired.fq.gz ./trim_out/output_forward_unpaired.fq.gz ./trim_out/output_reverse_paired.fq.gz ./trim_out/output_reverse_unpaired.fq.gz ILLUMINACLIP:/disk1/202031107010173/Biosofts/Trimmomatic-0.38/adapters/TruSeq2-PE.fa:2:30:10 SLIDINGWINDOW:5:20 LEADING:20 TRAILING:20 MINLEN:75
TrimmomaticPE: Started with arguments:
 -phred33 /disk/shares/Seqs/test_7942raw_1.fq.gz /disk/shares/Seqs/test_7942raw_2.fq.gz ./trim_out/output_forward_paired.fq.gz ./trim_out/output_forward_unpaired.fq.gz ./trim_out/output_reverse_paired.fq.gz ./trim_out/output_reverse_unpaired.fq.gz ILLUMINACLIP:/disk1/202031107010173/Biosofts/Trimmomatic-0.38/adapters/TruSeq2-PE.fa:2:30:10 SLIDINGWINDOW:5:20 LEADING:20 TRAILING:20 MINLEN:75
Multiple cores found: Using 4 threads
Using PrefixPair: 'AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT' and 'CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT'
Using Long Clipping Sequence: 'AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT'
Using Long Clipping Sequence: 'AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG'
Using Long Clipping Sequence: 'TTTTTTTTTTAATGATACGGCGACCACCGAGATCTACAC'
Using Long Clipping Sequence: 'TTTTTTTTTTCAAGCAGAAGACGGCATACGA'
Using Long Clipping Sequence: 'CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT'
Using Long Clipping Sequence: 'AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT'
ILLUMINACLIP: Using 1 prefix pairs, 6 forward/reverse sequences, 0 forward only sequences, 0 reverse only sequences
Exception in thread "main" java.io.FileNotFoundException: /disk/shares/Seqs/test_7942raw_1.fq.gz (No such file or directory)
        at java.io.FileInputStream.open0(Native Method)
        at java.io.FileInputStream.open(FileInputStream.java:195)
        at java.io.FileInputStream.<init>(FileInputStream.java:138)
        at org.usadellab.trimmomatic.fastq.FastqParser.parse(FastqParser.java:135)
        at org.usadellab.trimmomatic.TrimmomaticPE.process(TrimmomaticPE.java:265)
        at org.usadellab.trimmomatic.TrimmomaticPE.run(TrimmomaticPE.java:555)
        at org.usadellab.trimmomatic.Trimmomatic.main(Trimmomatic.java:80)

再次运行FastQC查看测试结果，